The invention relates to the production of modified polyglucans through the alteration of the polyglucan biosynthesis pathway.
Starch constitutes 65-75% of the corn kernel and is the main source of energy for livestock and poultry fed corn-based feed rations. Energy availability from corn is limited to a certain degree by endosperm matrix factors that prevent the release of intact starch granules during digestion. Protein and fiber characteristics may be manipulated to facilitate the release of starch granules, thereby enhancing energy availability.
Energy availability from corn is also determined by starch and oil content, starch structure (amylose:amylopectin ratio), and interactions among these different factors. Degradation characteristics of isolated starch are largely determined by the polyglucan structure. Waxy starch (all amylopectin), once gelatinized, is more rapidly digested than normal starch (70-75% amylopectin, 25-30% amylose). High amylose (70%) starch is more slowly and less expensively digested. Highly branched polysaccharides such as phytoglycogen are soluble and very rapidly digested. The enhanced in vitro digestibility of isolated starch from waxy corn over isolated starch from normal corn does not always translate to improved digestibility of ground corn (e.g., Ertl and Dale (1997) Appl. Poul. Res. 6:432-435), which is possibly caused by component interactions.
Starch can be converted into simple sugars by an enzymatic process carried out in two stages: the liquefaction of starch and the saccharification of the liquefied starch. See, for example, Manners (1985) xe2x80x9cStructural Analysis of Starch Components by Debranching Enzymes,xe2x80x9d in New Approaches to Research on Cereal Carbohydrates, ed. Hill (Amsterdam), pp. 45-54; and Enevoldsen (1985) xe2x80x9cAspects of the Fine Structure of Starchxe2x80x9d, in New Approaches to Research on Cereal Carbohydrates, ed. Hill (Amsterdam), pp. 55-60.
Amylopectin is a branched glucose polymer that is a major constituent of plant starch granules and the primary determinant of their structural and physical properties. The spatial positioning of xcex1(1xe2x86x926) glycosidic bonds, i.e., branch linkages, is a critical aspect of the three dimensional structure of amylopectin. Branch linkages are introduced by the actions of starch branching enzymes (BEs) and are hydrolyzed by the, actions of starch debranching enzymes (DBEs). See, for example, Preiss (1996) Starch Synthesis in Sinks and Sources (Marcell Dekker, Inc., New York), pp. 63-96; Smith et al. (1997) Annu. Rev. Plant Physiol. Plant Mol. Biol. 48:67-87. Mutations that result in DBE deficiencies, such as the sugary1 (su1) mutations of maize and rice (James et al. (1995) Plant Cell 7:417-429; Nakamura et al. (1996) Physiol. Plant. 97:491-498; Pan et al. (1984) Plant Physiol. 74:324-328; Rahman et al. (1998) Plant Physiol. 117:425-435), alter the number and spatial distribution of branches in amylopectin. DBEs, therefore, are believed to be involved in branch pattern determination, possibly providing an editing function (Ball. et al. (1996) Cell 86:349-352).
The two classes of DBEs that have been identified in plants and are distinguishable by their substrate specificity (Doehlert et al. (1991) J. Plant Physiol. 138:566-572; Lee et al. (1971) Arc. Biochem. Biophys. 143:365-374; and Lee et al. (1971) xe2x80x9cGlycogen and Starch Debranching Enzymes,xe2x80x9d The Enzymes, Vol. 3, ed. Boyer (Academic Press, New York), pp. 191-234. Isoamylases cleave xcex1(1xe2x86x926) branch linkages in amylopectin and glycogen but do not hydrolyze the chemically identical bonds in pullulan, an xcex1(1xe2x86x926)-linked maltotriose polymer. In contrast, pullulanases, also referred to as R-enzymes or limit-dextrinases (Manners (1997) J. Appl. Glycosci. 44:83-85), readily hydrolyze xcex1(1xe2x86x926) linkages of pullulan or amylopectin, but have little activity toward glycogen. Biochemical fractionation experiments identified both isoamylase and pullulanase activities in developing maize kernels during the starch biosynthetic period (Doehlert et al. (1991) J. Plant Physiol. 138:566-572; Pan et al. (1984) Plant Physiol. 74:324-328), but the specific functions of these two DBEs in polyglucan biosynthesis have not yet been established.
The primary sequences of a pullulanase from rice and maize endosperm are known from cloned cDNAs. Rice R-enzyme (RE) was purified biochemically and characterized as a pullulanase-type DBE, and the cDNA coding for RE was cloned (Nakamura et al. (1996) Planta 199:209-218; Toguri (1991) J. Plant Physiol. 137:541-546). A maize pullulanase, ZPU1, has also been cloned (Beatty et al. (1999) Plant Physiol. 119:255-266). In addition, a maize cDNA identified from a cloned fragment of the su1 gene codes for a protein similar to bacterial isoamylases (James et al. (1995) Plant Cell 7:417-429). The su1 gene product, SU1, functions as an isoarnylase-type DBE and is present in developing maize endosperm during the time that starch is synthesized (Rahman et al. (1998) Plant Physiol. 117:425-435).
Expression of the isoamylase- and pullulanase-type DBEs of maize seemingly is coordinately controlled. Even though the su1 gene codes for an isoamylase (Rahman et al. (1998) Plant Physiol. 117:425-435), previous studies have demonstrated a reduction in the activity of a pullulanase-type DBE in su1xe2x80x94mutant endosperms. (Pan et al. (1984) Plant Physiol. 74:324-328). Consistent with these data, a protein related immunologically to rice RE is present in nonmutant maize kernels at 20 days after pollination (DAP) but deficient in su1xe2x80x94mutant kernels of the same age (Rahman et al. (1998) Plant Physiol. 117:425-435). Thus, su1xe2x80x94mutations apparently result in the deficiency of two distinct DBEs. In rice, the su1 mutation controlling RE expression maps to a chromosomal location that is distinct from the gene that codes for RE (Nakamura et al. (1996) Planta 199:209-218). Accordingly, coordinated control of the amount of isoamylase and pullulanase protein (and activity) is seemingly operative in rice as well (Kubo et al. (1999) Plant Physiol. 121:399-409).
Mutations in su1 increase phytoglycogen content and produce several advantageous physical characteristics of polyglucan. For example, the accumulation of phytoglycogen in su1 mutants is associated with smaller and more numerous starch granules. In addition, a polyglucan containing a high phytoglycogen content has a reduced temperature of gelatinization compared to that of waxy or normal starch (Wang et al. (1992) Cereal Chem. 69:328-334). The reduced gelatinization temperature increases starch solubility after processing (grinding, pelleting, steam flaking) at temperatures below the gelatinization temperature of normal starch. The smaller granule size and reduced temperature of gelatinization may both contribute to the high digestibility of starch from sugary1 mutant corn. See, for example, Fuwa et al. (1979) J. Nutr. Sci. Vitaminol. 25:103-114 and Fuwa et al. (1979) Cereal Chem 54:230-237.
The relative importance of SU1 and ZPU1 in polyglucan debranching and the production of phytoglycogen is unclear, since protein levels and debranching activities of both enzymes are reduced in the su1 mutant. However, in rice the su1 mutation is primarily associated with a reduction in pullulanase activity and the reduction in the ratio of debranching to branching enzyme activities (Nakamura et al. (1997) Plant J. 12:143-153). This phenotype suggests that the reduction in pullulanase activity is important to the rice su1 phenotype (Kubo et al. (1999) Plant Physiol. 121:399-409).
The present invention combines the altered expression of a pullulanase debranching enzyme, preferably with various other alterations in the polyglucan biosynthesis pathway, to produce modified polyglucan having optimized energy availability for different classes of livestock and optimized adduct modification of glucan production for food and industrial use.
Methods and compositions are provided to modify the physical characteristics of polyglucan. In particular, the methods of the invention provide a method for modulating polyglucan biosynthesis in a plant or plant cell. The method comprises stably introducing into the genome of the plant or plant cell at least two DNA constructs. The first DNA construct comprises a nucleotide sequence operably linked to a promoter active in the plant. Expression of the nucleic molecule decreases pullulanase-type activity in the plant. The nucleotide sequence of the first DNA construct can further comprise: a nucleic acid molecule comprising a nucleotide sequence encoding a plant pullulanase-type polypeptide or fragment thereof; a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO:1; a nucleic acid molecule comprising a nucleotide sequence having at least 70% identity to the sequence of SEQ ID NO:1; a nucleic acid molecule comprising a nucleotide sequence hybridizing under stringent conditions to the sequence of SEQ ID NO:1; and a nucleic acid molecule comprising a nucleotide sequence having an antisense sequence corresponding to one of the above-mentioned sequences. The second DNA construct comprises a nucleotide sequence operably linked to a promoter active in the plant. Expression of the nucleic acid sequence of the second DNA construct modulates the activity of a polypeptide involved in polyglucan synthesis.
In one embodiment, the nucleic acid sequence of the second DNA construct decreases starch synthase activity in the plant. In another embodiment, the nucleic acid sequence of the second DNA construct decreases the activity of a starch branching enzyme in the plant. In another embodiment, the nucleic acid sequence of the second DNA construct decreases the activity of an isoamylase in the plant. In another embodiment, the nucleic acid sequence of the second DNA construct increases the activity of a glucan synthase in the plant. In another embodiment, the nucleic acid sequence of the second DNA construct increases the activity of an isoamylase in the plant.
The methods of the invention find use in increasing the rate of polyglucan digestion. The methods of the invention also find use in creating two distinct pools of polyglucan comprising soluble phytoglycogen and amylose-enriched starch. In addition, the methods of the invention find use in the production of cationic polyglucan and amphoteric polyglucan. Furthermore, methods find use in increasing extractable polyglucan content. Methods also include an improved method of wetmilling.
Compositions of the invention include an expression cassette comprising at least two DNA constructs. The first DNA construct comprises a nucleotide sequence operably linked to a promoter active in the plant, wherein expression of the nucleic acid sequence decreases pullulanase-type activity in the plant. The nucleotide sequence of the first DNA construct comprises a sequence that modulates the activity of a plant pullulanase-like enzyme or fragment thereof. In other embodiments, the nucleotide sequence comprises a sequence of SEQ ID NO:1 or fragment and variants thereof. The second DNA construct comprises a nucleotide sequence operably linked to a promoter active in the plant. Expression of the sequences of the second DNA construct modulates the activity of a polypeptide involved in polyglucan biosynthesis.
Compositions of the invention further include plants and plant cells having modified polyglucan structures. Compositions further comprise the seed and the polyglucan of the above mentioned plant and plant cells. Compositions of the invention further include beverages having carbohydrate compositions comprising the phytoglycogen produced from the methods of the present invention.
Compositions and methods are provided for the modification of polyglucan structure to produce a polyglucan or a grain with improved functional properties useful in a wide range of food and industrial applications. By xe2x80x9cpolyglucanxe2x80x9d is intended any polyglucan structure comprising glucose molecules connected by xcex11xe2x88x924 glycosidic bonds or xcex11xe2x88x924 and xcex11xe2x88x926 glycosidic bonds. Constituents of polyglucan comprise phytoglycogen and starch. Starch accumulates as a complex granular structure composed of polyglucan chains comprising amylopectin and amylose. Characteristics of Amylopectin include a high molecular weight (107-106Da) and a polyglucan chain containing approximately 5% xcex1xe2x88x921,6 branches. Amylose is a smaller linear molecule (molecular weight of 105-106Da) and contains very few xcex11,6 branches (less than 1%) (Ball et al. (1996) Cell 86:340-352). Another polyglucan structure is phytoglycogen, characterized as a highly branched water-soluble polysaccharide. The characteristics of amylose, amylopectin and phytoglycogen are further described in Nakamura et al. (1996) Plant Science 121:1-18 and in Helt et al. (1997) Plant Biochemistry and Molecular Biology, Oxford University Press, both of which are herein incorporated by reference. Modifications of polyglucan structure include but are not limited to a change in the branching pattern of the polyglucan (i.e. a change in the number of branches or the branch length), a change in the overall charge of the branches (for example, through an increase in glucan phosphorylation or an increase in glucan amine content), or any other modification that alters the solubility properties of the polyglucan when compared to an unmodified plant. Modification may also refer to an increase in the overall level of polyglucan produced when compared to an unmodified plant.
The present invention provides methods and compositions to simultaneously modulate the function of multiple proteins involved in the polyglucan biosynthesis pathway. Specifically, methods and compositions to modulate the activity of pullulanase are provided. More specifically, methods and compositions are provided to modulate the activity of pullulanase and the activity of another protein in the polyglucan biosynthesis pathway. The xe2x80x9cpolyglucan biosynthesis pathwayxe2x80x9d is intended to comprise any protein involved, either directly or indirectly, in the synthesis of the polyglucan molecule. Furthermore, the proteins of the polyglucan biosynthesis pathway can be obtained from any organism which synthesizes polyglucan either in the form of starch or glycogen.
Modifications in the pathway refer to a modulation in activity of a protein in the pathway. By xe2x80x9cmodulating activityxe2x80x9d is intended that the expression or the activity of a protein in the polyglucan biosynthesis pathway is altered in some manner. Modulating activity will result in either a decrease or an increase in the native protein levels of an enzyme in the polyglucan biosynthesis pathway and/or an increase or decrease in protein activity of the enzyme. Modulating activity also comprises expression of an enzyme normally not found in the plant. Thus, plants and plant cells are obtained that have altered levels of proteins of the polyglucan biosynthesis pathway. Such plants, plant cells, and plant tissues are xe2x80x9cmodifiedxe2x80x9d in that the activities of proteins in the polyglucan biosynthesis pathway are altered. As noted below, various methods are available for creating modified plants, plant cells, and plant tissues including transformation and transfection and breeding. Such techniques will lead to altered expression of proteins in the polyglucan biosynthesis pathway in the modified plant, plant cell or tissue.
The present invention provides methods to alter a xe2x80x9cpullulanase-typexe2x80x9d enzyme. By xe2x80x9cpullulanase-typexe2x80x9d enzyme is intended an enzyme that hydrolyzes xcex1(1xe2x86x926) linkages of pullulan or amylopectin. The enzyme is therefore a debranching or deramifying enzyme. The pullulanase enzyme, according to the invention, breaks down pullulan into maltotriose and amylopectin into linear polyglucan segments. The amino acid sequence of a pullulanase protein is characterized by six motifs conserved in all debranching enzymes (i.e. pullulanase and isoamylase). The pullulanase class of debranching enzymes contains five additional conserved amino acid motifs not found in the isoamylase class. Pullulanase activity has been identified in both plants and bacteria. Plants exhibiting pullulanase activity include maize, rice, oat, sorghum, barley, broad bean, spinach, pea, sugar beat, potato and wheat. For review see Nakamura (1996) Plant Science 121:1-18 and references cited therein. Nucleotide sequences encoding plant pullulanases have been isolated, for example, in maize (ZPU1) (Genbank Accession No. AF080567)(SEQ ID NO:1), barley (Genbank Accession No. AF022725), and spinach (Genbank Accession No. X83969). Each of these Genbank Accession Nos. is herein incorporated by reference.
In specific embodiments of the present invention the activity of the maize pullulanase, ZPU1, is modulated. The corn pullulanase gene (Zpu1) is weakly expressed as early as 12 and 14 DAP, and is strongly and uniformly expressed from 18 to at least 32 DAP. ZPU1 is related to rice DBE termed R-enzyme or limit-dextrinase. The proteins are immunologically cross-reactive and are approximately 77% identical in their amino acid sequences. The debranching enzyme is of the pullulanase-type, hydrolyzing alpha-(1xe2x86x926) branch linkages in branched polysaccharides. The ZPU1 protein is approximately 100 kD in size. ZPU1 is the product of the single-copy maize Zpu1 gene, which has been mapped to the central region of chromosome 2. The Zpu1 gene is transcribed in developing maize endosperm, and to a slight extent in maize embryo and tassel, but not leaves.
The present invention provides methods to simultaneously modulate the function of plant pullulanase and at least one other protein in the polyglucan biosynthesis pathway. Such proteins include, but are not limited to, soluble starch synthase, granule bound starch synthase, starch debranching enzymes, ADP glucose pyrophosphorylase, isoamylases, and starch branching enzymes. Other enzymes that may also be modulated and which can interact, either directly or indirectly, in polyglucan biosynthesis are glutamine:fructose-6-phosphate amidotransferase (GFAT), phosphoglucomutase, UDP-glucose pyrophosphorylase and glycogen synthase (Tarentino and Maley (1976) FEBS Lett. 69:175-178; Kirkman et al. (1989) BioFactors 2:123-126, both of which are herein incorporated by reference).
Starch synthase transfers a glucose residue from ADP-glucose to the OH-group in the 4-position of the terminal glucose molecule in the polysaccharide chain. Several plant granule-bound starch synthases are known in the art. Examples of granule-bound starch synthases include, but are not limited to, pea (Genbank Accession No. AF031162), barley (Genbank Accession No. X0793 1), potato (Genbank Accession Nos. 58453 and A23741), maize (Genbank Accession Nos. X03935 and 22509)(SEQ ID NO:3), sorghum (Genbank Accession No. U23945), sweet potato (Genbank Accession Nos. AF068834 and AF 111157), wheat (Genbank Accession No. D10657, AB019623), sugar beet (Genbank Accession No. AF173652), and rice (Genbank Accession Nos. AF092444, AF092443, and A1736032). Each of these Genbank Accession Nos. is herein incorporated by reference.
Variants of plant starch synthases include both loss of function, recessive, and gain of function, dominant, mutant alleles. For example, the major granule-bound starch synthase in maize is encoded by the Wx gene. Recessive mutations in Wx resulting in either the absence or a decrease in the granule-bound starch synthase activity have been identified (Nelson et al. (1968) Genetics 60:507-524, Shure et al. (1983) Cell 35:225-233, Wessler et al. (1985) PNAS 82:4177-4181, and Klosgen et al. (1986) Mol Gen Genet 203:237-244). Other variant of plant granule bound starch synthases include: the amf-1 from potato (Visser et al. (1989) Plant Science 64:185-192), the Wx-D1b null allele from wheat (Genbank Accession No. AF113844), and the Wx-A1 allele from wheat (Genbank Accession No. AF113843). Each of these Genbank Accession Nos. is herein incorporated by reference.
Glucan synthases incorporate UDP glucose into the polyglucan chain. Such enzymes are optimized for incorporation of amine-containing sugars and include, but are not limited to, glutamine:fructose-6-phosphate amidotransferase and mammalian glycogen synthase. See for example, Tarentino and Maley (1976) FEBS Lett. 69:175-178. Maize glutamine:fructose-6-phosphate amidotransferase sequences (SEQ ID NO:5) can be found in U.S. patent application Ser. No. 09/379,779, filed Aug. 24, 1999, herein incorporated by reference. Mammalian glycogen synthases are also known in the art and include, but are not limited to glycogen synthase from Mus Musculus (Genbank Accession No. X94616) and human liver glycogen synthase (Genbank Accession No. D29685)(SEQ ID NO:7). Each of these Genbank Accession Nos. is herein incorporated by reference. Branches on polyglucan are formed by branching enzymes. At certain chain lengths the polysaccharide chain is cleaved at the (xcex11xe2x86x924) glycosidic bond and the chain fragment thus separated is connected via a newly formed (xcex11xe2x86x926) to a neighboring chain. These chains are elongated further by starch synthase until a new chain develops. Starch branching enzymes from plants are composed of two isoforms, BEI and BEII. The two isoforms exhibit different kinetic and physio-chemical properties and their relative distribution depends on the plant species and the tissue. Nucleotide sequences encoding branching enzymes in plants are available, for example: barley starch branching enzyme IIb (Genbank Accession No. AF06456), and starch branching enzyme IIa (Genbank Accession No. AF064560), maize starch branching enzyme IIa (SBEIIa) (Genbank Accession Nos. 465948 and U65948)(SEQ ID NO:9), a potato starch branching enzyme (Genbank Accession No. A43341, A43340), rice branching enzyme-1 (Genbank Accession No. D11082), maize starch branching enzyme-1 (SBE1) (Genbank Accession Nos. D11081 and 217959)(SEQ ID NO:13), rice branching enzyme II (Genbank Accession No. X80010), rice branching enzyme I (Genbank Accession No. X80009), and maize starch branching enzyme IIb (SBEIIb) (Genbank Accession Nos. AAC33764 and AF02725)(SEQ ID NO:11). Each of these Genbank Accession Nos. is herein incorporated by reference.
Variants of plant starch branching enzymes include both dominant and recessive mutant alleles. For example, the maize amylose extender mutation (ae) gene, encodes branching enzyme IIb. See, for example, Gao et al. (1997) Plant Physiol 114:69-78; Burton et al. (1995) Plant J. 7:3-15). In addition, a transgenic mutation of maize starch branching enzyme I has also been identified (Lightner et al. (1999)415st Annual Maize Genetics Conference, March 11-14, Lake Geneva, Wis).
ADP-glucose pyrophosphorylase comprises multiple subunits and catalyzes the formation of ADP glucose. The subunits comprising this enzyme are known in the art and include, for example, sugar beet (Genbank Accession Nos. X78900 and X78899), sweet potato (Genbank Accession Nos. AJ24925 and AJ249256), barley (Genbank Accession No. AJ239130), sorghum (Genbank Accession No. U87452), rice U87450, maize (Genbank Accession Nos. M81603, S48563, and M79333) and soybean (Genbank Accession No. A1900360). Variant of ADP-glucose pyrophosphorylase include both dominant and recessive mutant alleles and include, for example, the alleles of the maize shrunken (Genbank Accession Nos. AF162682 and L35934) or alleles of the brittle gene from soybean (Genbank Accession No. A1900360) or from maize (Genbank Accession No. M79333). Each of these Genbank Accession Nos. is herein incorporated by reference.
Isoamylases cleave xcex1(1xe2x86x926) branch linkages in amylopectin and glycogen but do not hydrolyze the chemically identical bonds in pullulan. Plant isoamylases include, but are not limited to, potato (Genbank Accession No. AF142591), maize (SU1) (Genbank Accession Nos. D90908 and AF030882)(SEQ ID NO:15), and barley (Genbank Accession No. AF142589) are also known in the art. Each of these Genbank Accession Nos. is herein incorporated by reference.
It is recognized that the activity of a protein in the polyglucan biosynthesis pathway may be modulated indirectly. For example, mutations in the Dull gene of maize modulate expression of a maize soluble starch synthase isoform and a starch branching enzyme. See, for example, U.S. Pat. No. 5,675,064. Alternatively, activity may be indirectly modulated by altering the activity of a protein involved in a transcriptional or post-transcriptional regulatory event of a protein in the polyglucan biosynthesis pathway.
Several methods are available in the art for modulating the activity of the pullulanase and other polypeptides of the polyglucan biosynthesis pathway. Such methods include, but are not limited to: antisense downregulation, cosuppression, or overexpression via the insertion of one or more extra copies of the selected sequence into the genome.
Methods to assay for either an increase or decrease in activity of the various polypeptides involved in polyglucan biosynthesis are known in the art. For example, transcript levels can be assayed using standard molecular biology techniques. Alternatively, assays for enzymatic activity are also known in the art. For example, isoamylase activity can be measured by incubating the extract containing the isoamylase polypeptide with amylopectin in 50 mM Hepes-NaOH, pH 7.0, for 2 hours at 30xc2x0 C. An aliquot of this reaction is subsequently mixed with water and a 0.01 M I2/0.5 M KI solution. The change in A550 is measured relative to a blank amylopectin reaction lacking protein extract. See, for example, Beatty et al. (1999) Plant Physiology 119:255-266, herein incorporated by reference. Further assays for isoamylase activity can be found in U.S. Pat. No. 5,750,876, herein incorporated by reference.
Pullulanase-type activity can be assayed by incubating the extract containing the enzyme with pullulan and 50 mM citrate, pH 5.5, at 37xc2x0 C. Activity is assayed as a change of absorption (A550) relative to a blank pullulan reaction. See, for example, Beatty et al. (1999) Plant Physiology 119:255-266. Further assays for pullulanase-type enzymatic activity can be found in, for example, U.S. Pat. No. 5,736,375, herein incorporated by reference.
Assays for granule-bound starch synthases are also known in the art. Such assays include measuring the affinity for ADP glucose and glucan substrates, activation by amylopectin, and the processivity of glucan chain extension. Such assays can be found in, for example, Edwards et al. (1999) European J. Biochem. 266:724-736, herein incorporated by reference. Activity of starch branching enzymes can be assayed by monitoring the rate of branching amylose and the rate of branching amylopectin. Details regarding these assays can be found in, for example, Guan et al. (1994) Plant Physiology 104:1449-1453 and Guan et al. (1994) Cell Mol. Biol. 40:981-988, both of which are herein incorporated by reference. Assays for liver glycogen synthase are described in, for example, Wang et al. (1998) Chin. Med. J. 111:32-34, herein incorporated by reference.
Glutamine:fructose-6-phosphate amidotransferase catalyzes the rate-limiting step of the hexosamine biosynthetic pathway. Specifically, a GFAT enzyme catalyzes the formation of glucasamine-6-phosphate and glutamate from fructose-6-phosphate in glutamine. Assays to measure this activity in vitro are known in the art. For example, the-GFAT enzyme is incubated with substrate and the product glucosamine-6-phosphate is measured with a standard assay, such as a colormetric assay. For example, Bessal et al. (1972) Plant Physiology 49:977 describe an assay in which a sample containing the GFAT enzyme is mixed with D-fructose-6-phosphate and L-glutamine. The mixture is incubated at 30xc2x0 C. for 1.5 hours and boiled for 2 minutes to stop the reaction. Following centrifugation, an aliquot of the supernatant was analyzed for D-glucosamine-6-phosphate using a modification of the colormetric assay by Ghosh et al. (1960) J. Biol. Chem. 235:1265. Alternatively, GFAT enzyme activity can be measured using a radioenzymatic assay in which the enzyme converts radiolabeled fructose-6-phosphate to radiolabeled glucosamine-6-phosphate. Such assays are described in U.S. application Ser. No. 09/379,779 filed Aug. 24, 1999, herein incorporated by reference.
Fragments and variants of the nucleotide sequences and proteins encoded thereby can be used in the present invention. By xe2x80x9cfragmentxe2x80x9d is intended a portion of the nucleotide sequence or a portion of the amino acid sequence and hence protein encoded thereby. Fragments of a nucleotide sequence may encode protein fragments that retain the biological activity of the native protein and hence modulate polyglucan structure. Use of such fragments will increase the activity of the polypeptide in the cell. Alternatively, fragments of a nucleotide sequence that are useful as hybridization probes generally do not encode proteins retaining biological activity. Furthermore, fragments used to decrease the activity of a polypeptide involved in polyglucan biosynthesis using antisense or cosuppression technology also may not encode a polypeptide having biological activity. However, expression of such fragments do result in a decrease in activity of a polypeptide involved in polyglucan synthesis. Thus, fragments of a nucleotide sequence may range from at least about 20 nucleotides, about 50 nucleotides, about 100 nucleotides, and up to the full-length nucleotide sequence encoding the proteins of the invention.
A fragment of a nucleotide sequence that encodes a biologically active portion or a non-biologically active portion of a polyglucan biosynthesis protein of the invention will encode at least 15, 25, 30, 50, 100, 150, 200, or 250 contiguous amino acids, or up to the total number of amino acids present in a full-length protein of the invention. Fragments of a nucleotide sequence encoding a polyglucan biosynthesis protein that are useful as hybridization probes or PCR primers generally need not encode a biologically active portion of the protein. Similarly, nucleic acid fragments used to decrease the activity of the polyglucan biosynthesis polypeptide using antisense or cosuppression technology need not encode a polypeptide having biological activity. Such fragments of a nucleotide sequence may range from at least about 20 nucleotides, about 50 nucleotides, about 100 nucleotides, and up to the full length nucleotide sequence of the invention.
Thus, a fragment of a nucleotide sequence may encode a biologically active portion of a polyglucan biosynthesis protein, or it may be a fragment that can be used as a hybridization probe/PCR primer or using cosuppression or antisense technology as disclosed in more detail below. A biologically active portion of a polyglucan biosynthesis protein can be prepared by isolating a portion of one of the nucleotide sequences encoding a polyglucan biosynthesis protein, expressing the encoded portion of the protein (e.g., by recombinant expression in vitro), and assessing the activity of the encoded portion of the polyglucan biosynthesis protein. Nucleic acid molecules that are fragments of a nucleotide sequence that modulate the activity of a polypeptide involved in polyglucan biosynthesis comprise at least 16, 20, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 800, 900, 1,000, 1,100, 1,200, 1,300, or 1,400 nucleotides, or up to the number of nucleotides present in a full-length nucleotide sequence of the protein.
Alternatively, variants of nucleotide sequences that encode polypeptides involved in polyglucan biosynthesis need not retain biological activity of the encoded protein. Such sequences find use in cosuppression, antisense technology and breeding techniques using recessive mutations. Expression of such variant nucleotide sequences will result in a decrease in the activity of the targeted polypeptide involved in polyglucan biosynthesis. Assays to measure a decrease in activity include, for example, a decrease in transcript levels or enzymatic activity using various assays known in the art. Such variants will have about 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
By xe2x80x9cvariantsxe2x80x9d is intended substantially similar sequences. For nucleotide sequences, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of a protein in the polyglucan biosynthesis pathway. Naturally occurring allelic variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR) and hybridization techniques as outlined below. Variant nucleotide sequences also include synthetically derived nucleotide sequences, such as those generated, for example, by using site-directed mutagenesis but which still encode a protein in the polyglucan biosynthesis pathway. Generally, variants of a particular nucleotide sequence of the invention will have at least about 40%, 50%, 60%, 65%, 70%, generally at least about 75%, 80%, 85%, preferably at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, and more preferably at least about 98%, 99% or more sequence identity to that particular nucleotide sequence as determined by sequence alignment programs described elsewhere herein using default parameters.
By xe2x80x9cvariantxe2x80x9d protein is intended a protein derived from the native protein by deletion (so-called truncation) or addition of one or more amino acids to the N-terminal and/or C-terminal end of the native protein; deletion or addition of one or more amino acids at one or more sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein, that is, they modulate polyglucan structure. Such variants may result from, for example, genetic polymorphism or from human manipulation. Biologically active variants of a native protein in the polyglucan biosynthesis pathway will have at least about 40%, 50%, 60%, 65%, 70%, generally at least about 75%, 80%, 85%, preferably at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, and more preferably at least about 98%, 99% or more sequence identity to the amino acid sequence for the native protein as determined by sequence alignment programs described elsewhere herein using default parameters. A biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
The proteins of the invention may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art. For example, amino acid sequence variants of the polyglucan biosynthesis proteins can be prepared by mutations in the DNA. Methods for mutagenesis and nucleotide sequence alterations are well known in the art. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods in Enzymol. 154:367-382; U.S. Pat. No. 4,873,192; Walker and Gaastra, eds. (1983) Techniques in Molecular Biology (MacMillan Publishing Company, New York) and the references cited therein. Guidance as to appropriate amino acid substitutions that do not affect biological activity of the protein of interest may be found in the model of Dayhoff et al. (1978) Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington, D.C.), herein incorporated by reference. Conservative substitutions, such as exchanging one amino acid with another having similar properties, may be preferred.
Thus, the genes and nucleotide sequences used in the present invention include both the naturally occurring sequences as well as mutant forms. Likewise, the proteins of the invention encompass both naturally occurring proteins as well as variations and modified forms thereof. Such variants will continue to possess the desired ability to modulate polyglucan structure. Obviously, the mutations that will be made in the DNA encoding the variant must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure. See, EP Patent Application Publication No. 75,444.
The deletions, insertions, and substitutions of the protein sequences encompassed herein are not expected to produce radical changes in the characteristics of the protein. However, when it is difficult to predict the exact effect of the substitution, deletion, or insertion in advance of doing so, one skilled in the art will appreciate that the effect will be evaluated by routine screening assays. That is, the activity can be evaluated by assaying the characteristics of the polyglucan synthesized. See Experimental section for methods to analyze the physical properties of polyglucan. Alternatively, the enzymatic activity can be assayed using methods described herein.
Variant nucleotide sequences and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling. With such a procedure, one or more different polyglucan biosynthesis protein coding sequences can be manipulated to create a new protein possessing the desired properties. In this manner, libraries of recombinant polynucleotides are generated from a population of related sequence polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo. For example, using this approach, sequence motifs encoding a domain of interest may be shuffled between a gene encoding a polyglucan biosynthesis protein of the invention and other known polyglucan biosynthesis genes to obtain a new gene coding for a protein with an improved property of interest, such as an increased Km in the case of an enzyme. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Cramen et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) Proc. Nall. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.
The following terms are used to describe the sequence relationships between two or more nucleic acids or polynucleotides: (a) xe2x80x9creference sequencexe2x80x9d, (b) xe2x80x9ccomparison windowxe2x80x9d, (c) xe2x80x9csequence identityxe2x80x9d, (d) xe2x80x9cpercentage of sequence identityxe2x80x9d, and (e) xe2x80x9csubstantial identityxe2x80x9d.
(a) As used herein, xe2x80x9creference sequencexe2x80x9d is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence.
(b) As used herein, xe2x80x9ccomparison windowxe2x80x9d makes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Generally, the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100, or longer. Those of skill in the art understand that to avoid a high similarity to a reference sequence due to inclusion of gaps in the polynucleotide sequence a gap penalty is typically introduced and is subtracted from the number of matches.
Methods of alignment of sequences for comparison are well known in the art. Thus, the determination of percent identity between any two sequences can be accomplished using a mathematical algorithm. Non-limiting examples of such mathematical algorithms are the algorithm of Myers and Miller (1988) CABIOS 4:11-17; the local homology algorithm of Smith et al. (1981) Adv. Appl. Math. 2:482; the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453; the search-for-similarity-method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. 85:2444-2448; the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 872264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 30 90:5873-5877.
Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 8 (available from Genetics Computer Group (GCG), 575 Science Drive, Madison, Wis., USA). Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al. (1988) Gene 73:237-244 (1988); Higgins et al. (1989) CABIOS 5:151-153; Corpet et al. (1988) Nucleic Acids Res.16:10881-90; Huangetal. (1992) CABIOS8:155-65; and Pearson et al. (1994) Meth. Mol. Biol. 24:307-331. The ALIGN program is based on the algorithm of Myers and Miller (1988) supra. A PAM 120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used with the ALIGN program when comparing amino acid sequences. The BLAST programs of Altschul et al (1990) J. Mol. Biol. 215:403 are based on the algorithm of Karlin and Altschul (1990) supra. BLAST nucleotide searches can be performed with the BLASTN program, score=100, wordlength=12, to obtain nucleotide sequences homologous to a nucleotide sequence encoding a protein of the invention. BLAST protein searches can be performed with the BLASTX program, score=50, wordlength=3, to obtain amino acid sequences homologous to a protein or polypeptide of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g., BLASTN for nucleotide sequences, BLASTX for proteins) can be used. See http://www.ncbi.hlm.nih.gov. Alignment may also be performed manually by inspection.
Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity using GAP Weight of 50 and Length Weight of 3; % similarity using Gap Weight of 12 and Length Weight of 4, or any equivalent program. By xe2x80x9cequivalent programxe2x80x9d is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by the preferred program.
GAP uses the algorithm of Needleman and Wunsch (1970) J Mol. Biol. 48:443-453, to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP considers all possible alignments and gap positions and creates the alignment with the largest number of matched bases and the fewest gaps. It allows for the provision of a gap creation penalty and a gap extension penalty in units of matched bases. GAP must make a profit of gap creation penalty number of matches for each gap it inserts. If a gap extension penalty greater than zero is chosen, GAP must, in addition, make a profit for each gap inserted of the length of the gap times the gap extension penalty. Default gap creation penalty values and gap extension penalty values in Version 10 of the Wisconsin Genetics Software Package for protein sequences are 8 and 2, respectively. For nucleotide sequences the default gap creation penalty is 50 while the default gap extension penalty is 3. The gap creation and gap extension penalties can be expressed as an integer selected from the group of integers consisting of from 0 to 200. Thus, for example, the gap creation and gap extension penalties can be 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65 or greater.
GAP presents one member of the family of best alignments. There may be many members of this family, but no other member has a better quality. GAP displays four figures of merit for alignments: Quality, Ratio, Identity, and Similarity. The Quality is the metric maximized in order to align the sequences. Ratio is the quality divided by the number of bases in the shorter segment. Percent Identity is the percent of the symbols that actually match. Percent Similarity is the percent of the symbols that are similar. Symbols that are across from gaps are ignored. A similarity is scored when the scoring matrix value for a pair of symbols is greater than or equal to 0.50, the similarity threshold. The scoring matrix used in Version 10 of the Wisconsin Genetics Software Package is BLOSUM62 (see Henikoffand Henikoff(1989) Proc. Natl. Acad. Sci. USA 89:10915).
(c) As used herein, xe2x80x9csequence identityxe2x80x9d or xe2x80x9cidentityxe2x80x9d in the context of two nucleic acid or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have xe2x80x9csequence similarityxe2x80x9d or xe2x80x9csimilarityxe2x80x9d. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif.).
(d) As used herein, xe2x80x9cpercentage of sequence identityxe2x80x9d means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.
(e)(i) The term xe2x80x9csubstantial identityxe2x80x9d of polynucleotide sequences means that a polynucleotide comprises a sequence that has at least 70% sequence identity, preferably at least 80%, more preferably at least 90%, and most preferably at least 95%, compared to a reference sequence using one of the alignment programs described using standard parameters. One of skill in the art will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning, and the like. Substantial identity of amino acid sequences for these purposes normally means sequence identity of at least 60%, more preferably at least 70%, 80%, 90%, and most preferably at least 95%.
Another indication that nucleotide sequences are substantially identical is if two molecules hybridize to each other under stringent conditions. Generally, stringent conditions are selected to be about 56C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. However, stringent conditions encompass temperatures in the range of about 1xc2x0 C. to about 20xc2x0 C., depending upon the desired degree of stringency as otherwise qualified herein. Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides they encode are substantially identical. This may occur, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. One indication that two nucleic acid sequences are substantially identical is when the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the polypeptide encoded by the second nucleic acid.
(e)(ii) The term xe2x80x9csubstantial identityxe2x80x9d in the context of a peptide indicates that a peptide comprises a sequence with at least 70% sequence identity to a reference sequence, preferably 80%, more preferably 85%, most preferably at least 90% or 95% sequence identity to the reference sequence over a specified comparison window. Preferably, optimal alignment is conducted using the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453. An indication that two peptide sequences are substantially identical is that one peptide is immunologically reactive with antibodies raised against the second peptide. Thus, a peptide is substantially identical to a second peptide, for example, where the two peptides differ only by a conservative substitution. Peptides that are xe2x80x9csubstantially similarxe2x80x9d share sequences as noted above except that residue positions that are not identical may differ by conservative amino acid changes.
In a PCR approach, oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any plant of interest. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene-specific primers, vector-specific primers, partially-mismatched primers, and the like.
In hybridization techniques, all or part of a known nucleotide sequence is used as a probe that selectively hybridizes to other corresponding nucleotide sequences present in a population of cloned genomic DNA fragments or cDNA fragments (i.e., genomic or cDNA libraries) from a chosen organism. The hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as 32p, or any other detectable marker. Thus, for example, probes for hybridization can be made by labeling synthetic oligonucleotides based on the sequence encoding proteins of the polyglucan biosynthesis pathway. Methods for preparation of probes for hybridization and for construction of cDNA and genomic libraries are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
Hybridization of such sequences may be carried out under stringent conditions. By xe2x80x9cstringent conditionsxe2x80x9d or xe2x80x9cstringent hybridization conditionsxe2x80x9d is intended conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences that are 100% complementary to the probe can be identified (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing). Generally, a probe is less than about 1000 nucleotides in length, preferably less than 500 nucleotides in length.
Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30xc2x0 C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60xc2x0 C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37xc2x0 C., and a wash in 1xc3x97 to 2xc3x97SSC (20xc3x97SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55xc2x0 C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37xc2x0 C., and a wash in 0.5xc3x97 to 1xc3x97SSC at 55 to 60?C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37xc2x0 C., and a wash in 0.1xc3x97SSC at 60 to 65xc2x0 C. Duration of hybridization is generally less than about 24 hours, usually about 4 hours to about 12 hours.
Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: Tm=81.5xc2x0 C.+16.6 (log M)+0.41 (%GC)xe2x88x920.61 (% form)xe2x88x92500/L; where M is the molarity of monovalent cations, %GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Tm is reduced by about 1xc2x0 C. for each 1% of mismatching; thus, Tm, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with xe2x89xa790% identity are sought, the Tm can be decreased 10xc2x0 C. Generally, stringent conditions are selected to be about 5xc2x0 C. lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4xc2x0 C. lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10xc2x0 C. lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20xc2x0 C. lower than the thermal melting point (Tm). Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a Tm of less than 45xc2x0 C. (aqueous solution) or 32xc2x0 C. (formamide solution), it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biologyxe2x80x94Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, N.Y.); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
Thus, isolated sequences that encode for a protein of the polyglucan biosynthesis pathway and which hybridize under stringent conditions to the sequences encoding the polyglucan biosynthesis proteins disclosed herein, or to fragments thereof, are encompassed by the present invention. Such sequences will be at least about 40% to 50% homologous, about 60%, 65%, or 70% homologous, and even at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more homologous with the disclosed sequences. That is, the sequence identity of sequences may range, sharing at least about 40% to 50%, about 60%, 65%, or 70%, and even at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
The nucleotide sequence of the present invention that modulate the polyglucan biosynthesis pathway can be provided in expression cassettes for expression in a plant of interest. The expression cassette will include 5xe2x80x2 and 3xe2x80x2 regulatory sequences operably linked to a nucleic acid sequence encoding a pullulanase polypeptide or a nucleic acid sequence which, upon expression, downregulates the activity of the endogenous pullulanase enzyme. By xe2x80x9coperably linkedxe2x80x9d is intended a functional linkage between a promoter and a second sequence, wherein the promoter sequence initiates and mediates transcription of the DNA sequence corresponding to the second sequence. Generally, operably linked means that the nucleic acid sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame.
Specific embodiments of the present invention require at least one additional gene to be co-transformed into the organism. A single expression cassette may contain a pullulanase nucleic acid sequence that, upon expression, modulates activity of the nucleic acid sequence and at least one additional gene. Alternatively, the additional gene(s) can be provided on multiple expression cassettes. In specific embodiments, the additional genes co-transformed into the plant include nucleic acid sequences that, upon expression, modulate the activity of a polypeptide involved in the polyglucan biosynthesis pathway.
Such an expression cassette is provided with a plurality of restriction sites for insertion of the nucleic acid sequence encoding a protein of the polyglucan biosynthesis pathway to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.
The expression cassette will include in the 5xe2x80x2xe2x88x923xe2x80x2 direction of transcription, a transcriptional and translational initiation region, a coding sequence of the pullulanase protein and a transcriptional and translational termination region functional in plants. The transcriptional initiation region, the promoter, may be native or analogous or foreign or heterologous to the plant host. Additionally, the promoter may be the natural sequence or alternatively a synthetic sequence. By xe2x80x9cforeignxe2x80x9d is intended that the transcriptional initiation region is not found in the native plant into which the transcriptional initiation region is introduced.
While it may be preferable to express the sequences using heterologous promoters, the native promoter sequences may be used. Such constructs would change expression levels of the polyglucan biosynthesis proteins in the plant or plant cell. Thus, the phenotype of the plant or plant cell is altered.
The termination region may be native with the transcriptional initiation region, may be native with the operably linked DNA sequence of interest, or may be derived from another source. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Nucleic Acids Res.17:7891-7903; and Joshi et al. (1987) Nucleic Acid Res. 15:9627-9639.
Where appropriate, the nucleic acid sequence may be optimized for increased expression in the transformed plant. That is, the nucleic acid sequence can be synthesized using plant-preferred codons for improved expression. Methods are available in the art for synthesizing plant-preferred genes. See, for example, U.S. Pat. Nos. 5,380,831, and 5,436,391, and Murray et al. (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference.
Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences that may be deleterious to gene expression. The G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.
The expression cassettes may additionally contain 5xe2x80x2 leader sequences-in the expression cassette construct. Such leader sequences can act to enhance translation. Translation leaders are known in the art and include: picomavirus leaders, for example, EMCV leader (Encephalomyocarditis 5xe2x80x2 noncoding region) (Elroy-Stein et al. (1989) PNAS USA 86:6126-6130); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Allison et al. (1986); MDMV leader (Maize Dwarf Mosaic Virus); Virology 154:9-20), and human immunoglobulin heavy-chain binding protein (BiP), (Macejak et al. (1991) Nature 353:90-94); untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4) (Jobling et al. (1987) Nature 325:622-625); tobacco mosaic virus leader (TMV) (Gallie et al. (1989) in Molecular Biology of RNA, ed. Cech (Liss, N.Y.), pp. 237-256); and maize chlorotic mottle virus leader (MCMV) (Lommel et al. (1991) Virology 81:382-385). See also, Della-Cioppa et al. (1987) Plant Physiol. 84:965-968. Other methods known to enhance translation can also.be utilized, for example, introns, and the like.
In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved.
A number of promoters can be used in the practice of the invention. The promoters can be selected based on the desired outcome. The nucleic acids can be combined with constitutive, tissue-preferred, or other promoters for expression in plants.
Such constitutive promoters include, for example, the core promoter of the Rsyn7 (PCT application Serial No. U.S. Ser. No. 99/03,863); the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026), and the like. Other constitutive promoters include, for example, U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; and 5,608,142.
Tissue-preferred promoters can be utilized to target the expression of the pullulanase protein within a particular plant tissue. Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) Plant Physiol. 112(3):1331-1341; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini etal. (1996) Plant Physiol. 112(2):513-524; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Lam (1994) Results Probl. Cell Differ. 20:181-196; Orozco et al. (1993) Plant Mol Biol. 23(6):1129-1138; Matsuoka et al. (1993) Proc Natl. Acad. Sci. USA 90(20):9586-9590, and Guevara-Garcia et al. (1993) Plant J 4(3):495-505. Such promoters can be modified, if necessary, for weak expression. xe2x80x9cSeed-preferredxe2x80x9d promoters include both xe2x80x9cseed-specificxe2x80x9d promoters (those promoters active during seed development such as promoters of seed storage proteins) as well as xe2x80x9cseed-germinatingxe2x80x9d promoters (those promoters active during seed germination). See Thompson et al. (1989) BioEssays 10:108, herein incorporated by reference. Such seed-preferred promoters include, but are not limited to, Cim1 (cytokinin-induced message); cZ19B1 (maize 19 kDa zein); and ce1A (cellulose synthase). Gama-zein is a preferred endosperm-specific promoter. Glob-1 is a preferred embryo-specific promoter. For dicots, seed-specific promoters include, but are not limited to, bean xcex2-phaseolin, napin, xcex2-conglycinin, soybean lectin, cruciferin, and the like. For monocots, seed-specific promoters include, but are not limited to, maize 15 kDa zein, 22 kDa zein, 27 kDa zein, g-zein, waxy, shrunken 1, shrunken 2, globulin 1, etc.
Root-specific promoters are known and can be selected from the many available from the literature or isolated de novo from various compatible species. See, for example, Hire et al. (1992) Plant Mol. Biol. 20(2):207-218 (soybean root-specific glutamine synthetase gene); Keller and Baumgartner (1991) Plant Cell 3(10):1051-1061 (root-specific control element in the GRP 1.8 gene of French bean); Sanger et al. (1990) Plant Mol. Biol. 14(3):433-443 (root-specific promoter of the mannopine synthase (MAS) gene of Agrobacterium tumefaciens); and Miao et al. (1991) Plant Cell 3(l):11-22 (full-length cDNA clone encoding cytosolic glutamine synthetase (GS), which is expressed in roots and root nodules of soybean). See also Bogusz et al. (1990) Plant Cell 2(7):633-641, where two root-specific promoters isolated from hemoglobin genes from the nitrogen-fixing nonlegume Parasponia andersonii and the related non-nitrogen-fixing nonlegume Trema tomentosa are described. The promoters of these genes were linked to a xcex2-glucuronidase reporter gene and introduced into both the nonlegume Nicotiana tabacum and the legume Lotus corniculatus, and in both instances root-specific promoter activity was preserved. Leach and Aoyagi (1991) describe their analysis of the promoters of the highly expressed ro1C and ro1D root-inducing genes of Agrobacterium rhizogenes (see Plant Science (Limerick) 79(1):69-76). They concluded that enhancer and tissue-preferred DNA determinants are dissociated in those promoters. Teeri et al. (1989) used gene fusion to lacZ to show that the Agrobacterium T-DNA gene encoding octopine synthase is especially active in the epidermis of the root tip and that the TR2xe2x80x2 gene is root specific in the intact plant and stimulated by wounding in leaf tissue, an especially desirable combination of characteristics for use with an insecticidal or larvicidal gene (see EMBO J. 8(2):343-350). The TR1xe2x80x2 gene, fused to nptII (neomycin phosphotransferase II) showed similar characteristics. Additional root-preferred promoters include the VfENOD-GRP3 gene promoter (Kuster et al. (1995) Plant Mol. Biol. 29(4):759-772); and ro1B promoter (Capana et al. (1994) Plant Mol. Biol. 25(4):681-691. See also U.S. Pat. Nos. 5,837,876; 5,750,386; 5,633,363; 5,459,252; 5,401,836; 5,110,732; and 5,023,179.
In a specific embodiment, the nucleic acid sequence that modulates the activity of a polypeptide involved in the polyglucan biosynthesis pathway is targeted to the chloroplast and/or amyloplast for expression. In this manner, where the nucleic acid of interest is not directly inserted into the plastid, the expression cassette will additionally contain a nucleic acid encoding a transit peptide to direct the nucleic acid of interest to the plastid. Such transit peptides are known in the art. See, for example, Von Heijne et al. (1991) Plant Mol. Biol. Rep. 9:104-126; Clark et al. (1989) J. Biol. Chem. 264:17544-17550; Della-Cioppa et al. (1987) Plant Physiol. 84:965-968; Romer et al. (1993) Biochem. Biophys. Res. Commun. 196:1414-1421; and Shah et al. (1986) Science 233:478-481.
Plastid targeting sequences are known in the art and include the chloroplast small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco) (de Castro Silva Filho et al. (1996) Plant Mol. Biol. 30:769-780; Schnell et al. (1991) J. Bio. Chem. 266(5):3335-3342); 5-(enolpyruvyl)shikimate-3-phosphate synthase (EPSPS) (Archer et al. (1990) J. Bioenerg. Biomemb. 22(6):789-810); tryptophan synthase (Zhao et al. (1995) J. Biol. Chem. 270(11):6081-6087); plastocyanin (Lawrence et al. (1997) J. Biol. Chem. 272(33):20357-20363); chorismate synthase (Schmidt et al. (1993) J. Biol. Chem. 268(36):27447-27457); and the light harvesting chlorophyll a/b binding protein (LHBP) (Lamppa et al. (1988) J Biol. Chem. 263:14996-14999). See also Von Heijne et al. (1991) Plant Mol. Biol. Rep. 9:104-126; Clark et al. (1989) J. Biol. Chem. 264:17544-17550; Della-Cioppa et al. (1987) Plant Physiol. 84:965-968; Romer et al. (1993) Biochem. Biophys. Res. Commun. 196:1414-1421; and Shah et al. (1986) Science 233:478-481.
Methods for transformation of chloroplasts are known in the art. See, for example, Svab et al. (1990) Proc. Natl. Acad. Sci. USA 87:8526-8530; Svab and Maliga (1993) Proc. Natl. Acad. Sci. USA 90:913-917; Svab and Maliga (1993) EMBO J. 12:601-606. The method relies on particle gun delivery of DNA containing a selectable marker and targeting of the DNA to the plastid genome through homologous recombination. Additionally, plastid transformation can be accomplished by transactivation of a silent plastid-borne transgene by tissue-preferred expression of a nuclear-encoded and plastid-directed RNA polymerase. Such a system has been reported in McBride et al. (1994) Proc. Natl. Acad. Sci. USA 91:7301-7305.
The nucleic acids of interest to be targeted to the chloroplast and/or amyloplast may be optimized for expression in the plastid to account for differences in codon usage between the plant nucleus and this organelle. In this manner, the nucleic acids of interest may be synthesized using chloroplast-preferred codons. See, for example, U.S. Pat. No. 5,380,831, herein incorporated by reference.
Generally, the expression cassette will comprise a selectable marker gene for the selection of transformed cells. Selectable marker genes are utilized for the selection of transformed cells or tissues. Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D). See generally, Yarranton (1992) Curr. Opin. Biotech. 3:506-511; Christopherson et al. (1992) Proc. Natl. Acad. Sci. USA 89:6314-6318; Yao et al (1992) Cell 71:63-72; Reznikoff(1992) Mol. Microbiol. 6:2419-2422; Barkley et al. (1980) in The Operon, pp. 177-220; Hu et al. (1987) Cell 48:555-566; Brown et al. (1987) Cell 49:603-612; Figge et al. (1988) Cell 52:713-722; Deuschle et al. (1989) Proc. Natt. Acad. Aci. USA 86:5400-5404; Fuerst et al. (1989) Proc. Natl. Acad. Sci. USA 86:2549-2553; Deuschle et al. (1990) i Science 248:480-483; Gossen (1993) Ph.D. Thesis, University of Heidelberg; Reines et al. (1993) Proc. Natl. Acad. Sci. USA 90:1917-1921; Labow et al. (1990) Mol. Cell. Biol. 10:3343-3356; Zambretti et al. (1992) Proc. Natl. Acad. Sci. USA 89:3952-3956;.Baim et al. (1991) Proc. Natl. Acad. Sci. USA 88:5072-5076; Wyborski et al. (1991) Nucleic Acids Res. 19:4647-4653; Hillenand-Wissman (1989) Topics Mol. Struc. Biol. 10: 143-162; Degenkolb et al. (1991) Antimicrob. Agents Chemother. 35:1591-1595; Kleinschnidt et al. (1988) Biochemistry 27:1094-1104; Bonin (1993) Ph.D. Thesis, University of Heidelberg; Gossen et al. (1992) Proc. Natl. Acad. Sci. USA 89:5547-5551; Oliva et al. (1992) Antimicrob. Agents Chemother. 36:913-919; Hlavka et al. (1985) Handbook of Experimental Pharmacology, Vol. 78 (Springer-Verlag, Berlin); Gill et al. (1988) Nature 334:721-724. Such disclosures are herein incorporated by reference. The above list of selectable marker genes is not meant to be limiting. Any selectable marker gene can be used in the present invention.
In specific embodiments of the present invention, the nucleotide sequences of pullulanase and the other proteins of the polyglucan biosynthesis pathway can be used to generate antisense constructions, which are complementary to at least a portion of the messenger RNA (mRNA) encoding these proteins. Antisense nucleotides are constructed to hybridize with the corresponding mRNA. Modifications of the antisense sequences may be made as long as the sequences hybridize to and interfere with expression of the corresponding mRNA. In this manner, antisense constructions having 70%, preferably 80%, more preferably 85% sequence identity to the corresponding antisense sequences may be used. Furthermore, portions of the antisense nucleotides may be used to disrupt the expression of the target gene. Generally, sequences of at least 50 nucleotides, 100 nucleotides, 200 nucleotides, or greater may be used.
The nucleotide sequences of the present invention may also be used in the sense orientation to suppress the expression of endogenous genes in plants. Methods for suppressing gene expression in plants using nucleotide sequences in the sense orientation are known in the art. The methods generally involve transforming plants with a DNA construct comprising a promoter that drives expression in a plant operably linked to at least a portion of a nucleotide sequence that corresponds to the transcript of the endogenous gene. Typically, such a nucleotide sequence has substantial sequence identity to the sequence of the transcript of the endogenous gene, preferably greater than about 65% sequence identity, more preferably greater than about 85% sequence identity, most preferably greater than about 95% sequence identity. See, U.S. Pat. Nos. 5,283,184 and 5,034,323; herein incorporated by reference.
By xe2x80x9cintroducingxe2x80x9d sequences that modulate polyglucan biosynthesis into a target plant is intended any means for incorporating the sequence of interest into the target plant. Such means includes conventional breeding methods, genetic transformation methods, or other such means as may be available. The methods of the invention do not depend on a particular method for introducing a nucleotide construct to a plant, only that the nucleotide construct gains access to the interior of at least one cell of the plant. By xe2x80x9cstable transformationxe2x80x9d is intended that the nucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by progeny thereof. The cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that constitutive expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure constitutive expression of the desired phenotypic characteristic has been achieved.
Transformation protocols as well as protocols for introducing nucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. Suitable methods of introducing nucleotide sequences into plant cells and subsequent insertion into the plant genome include microinjiection (Crossway et al. (1986) Biotechniques 4:320-334), electroporation (Riggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium-mediated transformation (Townsend et al., U.S. Pat No. 5,563,055), direct gene transfer (Paszkowski et al. (1984) EMBO J. 3:2717-2722), and ballistic particle acceleration (see, for example, Sanford et al., U.S. Pat. No. 4,945,050; Tomes et al. (1995) xe2x80x9cDirect DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,xe2x80x9d in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); and McCabe et al. (1988) Biotechnology 6:923-926). Also see Weissinger et al. (1988) Ann. Rev. Genet. 22:421-477; Sanford et al. (1987) Particulate Science and Technology 5:27-37 (onion); Christou et al. (1988) Plant Physiol. 87:671-674 (soybean); McCabe et al. (1988) Bio/Technology 6:923-926 (soybean); Finer and McMullen (1991) In vitro Cell Dev. Biol. 27P:175-182 (soybean); Singh et al. (1998) Theor. Appl. Genet. 96:319-324 (soybean); Datta et al. (1990) Biotechnology 8:736-740 (rice); Klein et al. (1988) Proc. Natl. Acad. Sci. USA 85:4305-4309 (maize); Klein et al. (1988) Biotechnology 6:559-563 (maize); Tomes, U.S. Pat. No. 5,240,855; Buising et al., U.S. Pat. Nos. 5,322,783 and 5,324,646; Tomes et al. (1995) xe2x80x9cDirect DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,xe2x80x9d in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg (Springer-Verlag, Berlin) (maize); Klein et al. (1988) Plant Physiol. 91:440-444 (maize); Fromm et al. (1990) Biotechnology8:833-839 (maize); Hooykaas-Van Slogteren et al. (1984) Nature (London) 311:763-764; Bytebier et al. (1987) Proc. Natl. Acad. Sci. USA 84:5345-5349 (Liliaceae); De Wet et al. (1985) in The Experimental Manipulation of Ovule Tissues, ed. Chapman et al. (Longman, N.Y.), pp. 197-209 (pollen); Kaeppler et al. (1990) Plant Cell Reports 15 9:415-418 and Kaeppler et al. (1992) Theor. Appl. Genet. 84:560-566 (whisker-mediated transformation); D""Halluin et al. (1992) Plant Cell 4:1495-1505 (electroporation); Li et al. (1993) Plant Cell Reports 12:250-255 and Christou and Ford (1995) Annals of Botany 75:407-413 (rice); Osjoda et al. (1996) Nature Biotechnology 14:745-750 (maize via Agrobacterium tumefaciens); all of which are herein incorporated by reference.
The cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that constitutive expression of the desired phenotypic characteristic is stably maintained and inherited and thenseeds harvested to ensure constitutive expression of the desired phenotypic characteristic has been achieved.
The present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Examples of plants of interest include, but are not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee (Coffea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea americana), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley, vegetables, ornamentals, and conifers.
Vegetables include tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo). Ornamentals include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum. Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata); Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga canadensis); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis). Preferably, plants of the present invention are crop plants (for example, corn, alfalfa, sunflower, Brassica, soybean, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, etc.), more preferably corn and soybean plants, yet more preferably corn plants.
Plants of particular interest include grain plants that provide seeds of interest, oil-seed plants, and leguminous plants. Seeds of interest include grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc. Oil seed plants include cotton, soybean, safflower, sunflower, Brassica, maize, alfalfa, palm, coconut, etc. Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc.
Embodiments of the present invention produce transgenic plants that combine modulating pullulanase debranching activity and at least one other protein of the polyglucan biosynthesis pathway. A decreased pullulanase activity will produce high levels of free sugars and increased levels of a highly branched polysaccharide (phytoglycogen) in the maize endosperm. By xe2x80x9cincreased levelsxe2x80x9d it is intended an increase in phytoglycogen content by about 15% to about 50%, particularly about 20% to about 30% over that found in an unmodified plant. Phytoglycogen is water-soluble, as are the free sugars, and is more readily available to digestion than granular starch of which the release is restricted by matrix factors in the kernel. In addition, reduction of pullulanase activity will reduce starch granule size, which will increase the effective surface area and further enhance the rate of enzymatic digestion. For example, using the automated in vitro gas measurement system described by Pell and Schofield (1993) J. Dairy Sci 76:1063-1073 and Schofield and Pell (1995) J. Anim. Sci 73:3455-3463, we have discovered the rate of digestion of phytoglycogen to be 34% higher than that of isolated corn starch (5.89 versus 4.38 ml/h). Thus, the available energy for monogastric and ruminant livestock is elevated in corn producing high levels of phytoglycogen.
Furthermore, reduction of pullulanase activity may produce starch granules which display a reduced temperature of gelatinization that would increase starch solubility during processing (grinding, pelleting, steam flaking) at temperatures below the gelatinization temperature of normal starch. The reduced gelatinization temperature would elevate the degree of starch gelatinization in processed feed and hence, starch digestibility, and reduce the energy required in feed processing (grinding, pelleting, steam-flanking).
Production of controlled levels of rapidly fermentable sugars and/or phytoglycogen in corn grain will also ensure adequate levels of fermentable carbohydrate in silage made from whole corn plants, and will provide corn to be used in silage additive to high protein silage. Such corn will provide the rapidly fermentable carbohydrates required for lactic acid formation to improve preservation, palatability, and nutritional value silage made from high protein forage. For corn silage, by xe2x80x9ccontrolled levelsxe2x80x9d is intended about a 5% to about 30%, particularly about a 5% to about 10% increase in phytoglycogen and/or rapidly fermentable sugars over that found in an unmodified plant. For corn grain to be used as an additive to high protein silages, by xe2x80x9ccontrolled levelsxe2x80x9d is intended about 5% to about 30%, particularly from about 20-30% increase in phytoglycogen and/or rapidly fermentable sugars over that found in an unmodified plant. xe2x80x9cHigh protein silagesxe2x80x9d comprises silages prepared from legumes including but not limited to alfalfa and red clover.
Polyglucan structure may be modified further by modulating the activity of at least one additional enzyme of the polyglucan biosynthesis pathway. In an embodiment of the present invention, the rate of carbohydrate digestion is further increased by combining the decreased pullulanase activity with the waxy trait (all amylopectin starch). By xe2x80x9cincreasexe2x80x9d is intended the rate of polyglucan digestion is about 5% to about 15%, from about 15% to about 25%, preferably from about 25% to about 35%, and more preferably from about 35% to 50% or greater than that of isolated polyglucan from an unmodified plant. Methods for measuring the rate of polyglucan digestion are known in the art and described in Pell and Schofield (1993) J. Dairy Sci 76:1063-1073 and in Schofield and Pell (1995) J. Anim. Sci 73:3455-3463, both of which are herein incorporated by reference. The approach could be entirely transgenic (suppressing expression of both pullulanase and a granule bound starch synthase) or by transferring the waxy mutation into a newly obtained transgenic plant with a decreased pullulanase activity. In a specific embodiment, the waxy trait is conferred by the granule-bound starch synthase, GBSSI, of maize and the pullulanase is ZPU1 of maize.
In another embodiment, the rate of polyglucan digestion is increased by combining the decreased pullulanase activity with a decreased isoamylase activity. The approach can be entirely transgenic (suppressing both pullulanase and isoamylase or by transferring the sugary mutation into a newly obtained transgenic plant with decreased pullulanase activity. In a specific embodiment, the sugary trait is conferred by disrupting the activity of the isoamylase, SU1 of maize, and the pullulanase activity disrupted is that of maize ZPU1.
Another embodiment of the present invention combines a decreased pullulanase activity with an increased amylose trait. By xe2x80x9cincreasedxe2x80x9d it is intended about 40% to about 95%, particularly about 40% to about 70% of the starch is amylose. The approach will create two distinct pools of carbohydrates (soluble phytoglycogen and amylose-enriched starch) to optimize energy utilization by ruminant livestock. Of these two carbohydrate pools, the soluble sugars and phytoglycogen will supply rumen microorganisms with easily fermnentable carbohydrate and the high amylose starch would be partly protected from degradation in the rumen but still available for digestion in the small intestine. The approach could be entirely transgenic (suppressing expression of both pullulanase and one of several starch branching enzymes) or by transferring a starch branching enzyme mutation into a newly obtained transgenic plant with a decreased pullulanase activity. In a specific embodiment, the mutation that alters starch branching enzyme activity is the maize SBEI, SBEIIa, or SBEIIb and the pullulanase is ZPU1 of maize. In another specific embodiment the decrease in starch branching enzyme activity is conferred by a transgenic mutation of maize starch branching enzyme-I (Lightner et al. (1999) 41 st Annual Maize Genetics Conference, March 11-14, Lake Geneva, Wis.).
The phosphorylation levels of glucans in starch granules may be increased upon reduction of pullulanase activity. Starch granule phosphate levels are elevated in sugary starch (Morrison and Karkalas (1990) In: Methods in Plant Biochemistry Vol.2), which could be dependent upon pullulanase activity, since pullulanase is involved in the branching pattern and there is a relationship between the degree of polyglucan phosphorylation and chain length distribution in amylopectin (Bennow et al. (1998) Carb. Res. 307:45-54). We have reconfirmed this, and have also discovered that the level of phosphorylation is even greater in phytoglycogen from sugary1: the phosphorous levels we measured were 1.6, 5.8, and 25.1 mg % P in lipid-free corn amylopectin, sugary starch, and phytoglycogen, respectively.
An expected outcome of a reduction in pullulanase activity would be the elicitation of the phosphorylation mechanism, which in turn would lead to about a 2-fold or higher increase in the level of covalent phosphorylation of xcex11,4-xcex11,6 glucan found within starch granules. This in turn may alter the branching pattern of amnylopectin. Industrial applications involving polyglucan phosphates are described in, for example, Rutenberg and Solarek (1984) Starch: Chemistry and Technology, R. L. Whistler et al., eds, Academic Press and Solarek (1986) Modified Starches: Properties and Uses, O. B. Wurzburg, ed. CRC Press, both of which are herein incorporated by reference. 
In an embodiment of the present invention, the charge of the polyglucan is modified. In this embodiment, the increased phosphorylation levels of the 1,4-1,6 glucan in the presence of reduced pullulanase activity is used in combination with transgenic plants containing glucan synthases optimized for the incorporation of amine-containing sugars into the polyglucan chain. The approach can be entirely transgenic, suppressing expression of pullulanase while overexpressing a glycogen synthase. In a specific embodiment the pullulanase suppressed is maize ZPU1 and the glycogen synthase is maize glutamine:fructose-6-phosphate amidotransferase or human liver glycogen synthase. This approach can produce amphoteric polysaccharides which have uses in several non-feed applications, including but not limited to explosives, oil field chemicals, textile fibers, personal care products, agricultural chemicals cosmetics and, most notably, paper manufacturing. See, for example, U.S. patent application No. 5,378,830 and Wurzburg, ed. (1986) Modified Starches: Properties and Uses, CRC Press, both of which are herein incorporated by reference.
Alternatively, the increased incorporation of the amines into the polyglucan can produce a cationic polyglucan that disrupts ordinary formation of starch. The suppression of pullulanase activity could enhance the ability of the cell to divert assimilates into the synthesis of phytoglycogen, a polymer that would be desired in this application and one that does not require integration into granules.
A further embodiment of the present invention maximizes starch accumulation in corn endosperm (at the expense of soluble sugars and polysaccharides) by increasing the levels of starch debranching enzymes and thereby reducing starch solubility. Cutting the normal levels of soluble sugars plus phytoglycogen (3-5%) in half will increase starch content, and presumably extractable starch, by about 1-2 percentage points, about 2% to about 4% and from about 4% to about 10%. The grain from such plants would therefore offer an improved method of wet milling. By xe2x80x9cwet millingxe2x80x9d is intended a method of obtaining polyglucan from plants. Wet milling is a multi-step process involving steeping and grinding kernels and separating the kernels into starch, protein, oil, and fiber fractions. A review of the maize wet milling process is given by S. R. Eckhoff in the Proceedings of the 4th Corn Utilization Conference, Jun. 24-26, 1992, St. Louis, Mo., printed by the National Corn Growers Association, CIBA-GEIGY Seed Division, and the USDA. This approach can be achieved by overexpression of pullulanase, preferably maize Zpu1. Alternatively, this approach can be achieved by generating a transgenic plant that overexpresses a pullulanase and an isoamylase. In specific embodiments, the pullulanase and isoamylase is from a plant, preferably maize ZPU1 and SU1.
A further embodiment comprises the use of phytoglycogen in beverages, such as in sports drinks. Digestion and absorption patterns of phytoglycogen are expected to be intermediate between those of soluble sugars and starch, resulting in lower glycemic indices than those obtained with sugars. Therefore, phytoglycogen may be used as an ingredient for beverages that require a rapid but sustained-release carbohydrate. Plants having reduced pullulanase or pullulanase and isoamylase activity would be produced for the purpose of generating grain enriched in water soluble phytoglycogen. This approach will result in an increase in phytoglycogen content. By xe2x80x9cincreasexe2x80x9d is intended an increase in phytoglycogen content of about 15% to about 50%, particularly about 20% to about 30% over that found in an unmodified plant. The approach could be entirely transgenic (suppressing expression of pullulanase and isoamylase) or by transferring a sugary mutation into a newly obtained transgenic plant with a decreased pullulanase activity. In a specific embodiment, the sugary trait is conferred by disrupting the activity of the isoamylase, SU1 of maize, and the pullulanase activity disrupted is that of maize ZPU1.